Hepatitis C virus (HCV) is the major etiological agent of post-transfusion and community-acquired non-A non-B hepatitis worldwide. It is estimated that over 200 million people worldwide are infected by the virus. A high percentage of carriers become chronically infected and many progress to chronic liver disease, so called chronic hepatitis C. This group is in turn at high risk for serious liver disease such as liver cirrhosis, hepatocellular carcinoma and terminal liver disease leading to death.
The mechanism by which HCV establishes viral persistence and causes a high rate of chronic liver disease has not been thoroughly elucidated. It is not known how HCV interacts with and evades the host immune system.
HCV is an enveloped positive strand RNA virus in the Flaviviridae family. The single strand HCV RNA genome is of positive polarity and comprises one open reading frame (ORF) of approximately 9600 nucleotides in length, which encodes a linear polyprotein of approx. 3010 amino acids. In infected cells, this polyprotein is cleaved at multiple sites by cellular and viral proteases to produce structural and non-structural (NS) proteins. The structural proteins (C, E1, E2 and E2-p7) comprise polypeptides that constitute the virus particle (Hijikata, M. et al., 1991, Proc. Natl. Acad. Sci. USA. 88, 5547-5551; Grakoui, A. et al., 1993(a), J. Virol. 67,1385-1395). The non-structural proteins (NS2, NS3, NS4A, NS4B, NS5A, NS5B) encode for enzymes or accessory factors that catalyze and regulate the replication of the HCV RNA genome. Processing of the structural proteins is catalyzed by host cell proteases (Hijikata et al., 1991, supra). The generation of the mature non-structural proteins is catalyzed by two virally encoded proteases. The first is the NS2/3 zinc-dependent metalloprotease which auto-catalyses the release of the NS3 protein from the polyprotein. The released NS3 contains a N-terminal serine protease domain (Grakoui A, et al., 1993(b), Proc Natl Acad Sci USA, 90, 10583-7; Hijikata, M. et al., 1993, J. Virol. 67, 4665-4675.) and catalyzes the remaining cleavages from the polyprotein. The released NS4A protein has at least two roles. First, forming a stable complex with NS3 protein and assisting in the membrane localization of the NS3/NS4A complex (Kim et al., Arch Virol. 1999, 144: 329-343) and second, acting as a cofactor for NS3 protease activity. This membrane-associated complex, in turn catalyzes the cleavage of the remaining sites on the polyprotein, thus effecting the release of NS4B, NS5A and NS5B (Bartenschlager, R. et al., 1993, J. Virol., 67, 3835-3844; Grakoui et al., 1993(a) supra; Hijikata et al., 1993 supra; Love, R. A. et al., 1996, Cell, 87, 331-342; reviewed in Kwong AD. et al., 1998, Antiviral Res., 40, 1-18). The C-terminal segment of the NS3 protein also harbors nucleoside triphosphatase and RNA helicase activity (Kim, D. W. et al., 1995, Biochem. Biophys. Res. Comm., 215,160-166). The function of the protein NS4B is unknown. NS5A, a highly phosphorylated protein, seems to be responsible for the Interferon resistance of various HCV genotypes (Gale Jr. et al. 1997 Virology 230, 217; Reed et al., 1997, J. Virol. 71, 7187). NS5B is an RNA-dependent RNA polymerase (RdRp) that is involved in the replication of HCV.
To better understand the mechanism of HCV RNA replication and to develop appropriate in vitro systems, biochemical analyses of the NS5B protein have been performed. Full-length NS5B has been produced and purified as a non-fusion protein from insect cells infected with recombinant baculovirus (S. -E. Behrens et al., 1996, EMBO J., 15:12-22; R. de Francesco et al, 1996, Methods Enzymol., 275:58-67) or as a tagged protein from both insect cells (V. Lohmann et al., 1997, J. Virol., 71:8416-8428; V. Lohmann et al., 1998, Virology 249:108-118) and E. coli (Z. -H. Yuan et al, 1997, BBRC 232:231-235). In vitro, the RdRp activity of recombinant NS5B is dependent on an RNA template and requires RNA or DNA as a primer (S. -E. Behrens et al, 1996, EMBO J. 15:12-22; V. Lohmann et al., 1997, J. Virol., 71:8416-8428). On RNA templates of heteropolymeric sequences, the 3′-OH of the template is used as a primer and elongation proceeds via a “snap-back” mechanism, leading to a double-stranded molecule in which template and product RNA are covalently linked (S. -E. Behrens et a., 1996, EMBO J., 15:12-22; V. Lohman et al., 1998, Virology, 249:108-118; G. Luo et al., 2000, J. Virol. 74:851-863). Recently, several groups also demonstrated that the HCV NS5B protein is able to initiate RNA synthesis de novo (J. Oh et al, 1999, J. Virol. 73:7694-7702; X. Sun et al., 2000, BBRC 268:798-803; W. Zhong et al., 2000, J. Virol. 74:2017-2022).
The NS5B RdRp has been crystallized to reveal a structure reminiscent of other nucleic acid polymerases (S. Bressanelli et al., 1999, PNAS USA 96:13034-13039; H. Ago et al., 1999, Structure 7:1417-1426; C. A. Lesburg et al, 1999, Nature Struct. Biol., 6:937-943). A comprehensive understanding of the differences between HCV and cellular polymerases will facilitate the design of specific inhibitors of HCV replication. Detailed kinetic information will also help in understanding the molecular basis of HCV NS5B-catalyzed nucleotide incorporation and subsequently the mechanistic characterization of the inhibitors.
Previous studies (S. -E. Behrens et a., 1996, EMBO J. 15:12-22; R. de Francesco et al., 1996, Methods Enzymol. 275:58-67; V. Lohmann et al., 1997, J. Virol. 71:8416-8428; V. Lohmann et al., 1998, Virology 249:108-118) provided little information with regard to the proportion of the polymerase RNA complexes that are competent for catalysis. Some recent studies investigated the template and primer requirements for HCV NS5B-directed RNA replication. Templates with 3′-termini free of secondary structures and short primers 2 or 3 nucleotides (nt) long were preferred for efficient initiation of RNA synthesis (W. Zhong et a., 2000, J. Virol. 74:9134-9143). In de novo initiation of RNA synthesis, however, NS5B needs a template with a stable secondary structure and a single-stranded sequence that contains at least one 3′-cytidylate.
Viral polymerases represent attractive targets for therapeutic inhibition of viral replication. The discovery of new antiviral agents often involves screening of large numbers of samples for inhibition of the target activity using either in vitro or in vivo assays. In general, polymerases are assayed by monitoring the incorporation of either 3H—, α-32P or α-33P-labeled mononucleotides into oligonucleotide products, or by the extension of 5′-end-labeled primers. Products incorporated into the extended primers are captured or separated using common filter assays, acid precipitation, or denaturing gel electrophoresis.
The HCV NS5B polymerase is a prime target in the search for inhibitors of HCV replication. Different preparations of the HCV polymerase exhibit varying efficiencies of product formation with a variety of RNA substrates. Moreover, the activity of purified recombinant NS5B polymerase varies significantly with specific RNA substrates. In addition, the in vitro RNA polymerase activity of NS5B is extremely sensitive to ionic strength, and salt concentrations exceeding 100 mM inhibit the reaction. Hence the ability to determine the potency of inhibitors at various salt concentrations is restricted by this limitation of standard enzymatic reactions. Also, HCV polymerase enzymatic assays disclosed in the prior art provide IC50 values as representative measurements of inhibitor potencies. For inhibitors that are competitive with either RNA or NTP, the IC50 value is proportional to the concentration of substrates in the assay and will vary depending on the concentration of these components.
In an effort to overcome the limitations of HCV polymerase assays that use sub-optimal and poorly characterized RNA substrates, the Applicants have developed an assay for identifying specific inhibitors of the HCV polymerase that is independent of RNA.
It is therefore an advantage of the present invention to provide an assay that permits a direct measurement of inhibitor potencies (reflected by Kd values as an unequivocal determination of inhibitor potency) under defined conditions, irrespective of the substrate concentration.
The direct binding assay of this invention is amenable to adjustments in salt concentration or pH levels beyond the restricted range required for RNA polymerization. This type of assay is amenable to a high sensitivity and a high throughput format.
It is a further advantage of the present invention to provide a probe that binds to the polymerase with a high affinity, and which is displaced by inhibitors of the enzyme.
It is a further advantage to provide an assay that is applicable to HCV polymerases of different genotypes.